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<div class="title">TreeBuilderManager.hpp</div>  </div>
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<a href="_tree_builder_manager_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="_distance_reader_ext_mem_8hpp.html">DistanceReaderExtMem.hpp</a>&quot;</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="_distance_reader_8hpp.html">DistanceReader.hpp</a>&quot;</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="_exception_handler_8hpp.html">ExceptionHandler.hpp</a>&quot;</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="_sequence_file_reader_8hpp.html">SequenceFileReader.hpp</a>&quot;</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="_tree_builder_bin_heap_8hpp.html">TreeBuilderBinHeap.hpp</a>&quot;</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="_tree_builder_ext_mem_8hpp.html">TreeBuilderExtMem.hpp</a>&quot;</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="_tree_node_8hpp.html">TreeNode.hpp</a>&quot;</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160; </div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="preprocessor">#include &lt;cstdlib&gt;</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160; </div>
<div class="line"><a name="l00011"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html">   11</a></span>&#160;<span class="keyword">class </span><a class="code" href="class_tree_builder_manager.html">TreeBuilderManager</a> {</div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;    <span class="keyword">struct </span>Float {</div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;        <span class="keywordtype">float</span> *pointer;</div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;        <span class="keywordtype">int</span> length;</div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;    };</div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160; </div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160; </div>
<div class="line"><a name="l00019"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68">   19</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68">InputType</a> {</div>
<div class="line"><a name="l00020"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68a5496170f117c3d558853e10ccee02666">   20</a></span>&#160;        <a class="code" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68a5496170f117c3d558853e10ccee02666">alignment</a>, <a class="code" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68a6d9503e62c1cc7af8faafe95ca03fa9f">distance</a></div>
<div class="line"><a name="l00021"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68a6d9503e62c1cc7af8faafe95ca03fa9f">   21</a></span>&#160;    };</div>
<div class="line"><a name="l00022"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008">   22</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008">AlphabetType</a> {</div>
<div class="line"><a name="l00023"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008a9cf0eb2046097228c5269e9da5e47cba">   23</a></span>&#160;        <a class="code" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008a9cf0eb2046097228c5269e9da5e47cba">dna</a>, <a class="code" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008a089be0a828fca4605323da2e3a171202">amino</a>, <span class="keyword">null</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008a229d43ec692cb711e87fa15d1a163c4a">   24</a></span>&#160;    };</div>
<div class="line"><a name="l00025"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8d">   25</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8d">CorrectionType</a> {</div>
<div class="line"><a name="l00026"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8da6a180df7a39a3dd2e0f2283fbdc9c9eb">   26</a></span>&#160;        <a class="code" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8da6a180df7a39a3dd2e0f2283fbdc9c9eb">not_assigned</a>, <a class="code" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8daa48e32132856572cccb189cd72e521c7">none</a>, <a class="code" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8da78e91f6ce40102b0d61e8b9d51750638">JukesCantor</a><span class="comment">/*DNA*/</span>, <a class="code" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8dae1e7c68b84de2d982d8fc029b480cc17">Kimura2</a><span class="comment">/*DNA*/</span>, <a class="code" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8da7bff75f1893babce718611848369ad04">FastTree</a> <span class="comment">/*amino*/</span>};</div>
<div class="line"><a name="l00027"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17">   27</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17">OutputType</a> {</div>
<div class="line"><a name="l00028"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17a19cba20113304d5be5b0b1b3cdb11b91">   28</a></span>&#160;        <a class="code" href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17a19cba20113304d5be5b0b1b3cdb11b91">dist</a>, <a class="code" href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17a432f48fbf28ef0573a1a3848b5cf1d40">tree</a></div>
<div class="line"><a name="l00029"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17a432f48fbf28ef0573a1a3848b5cf1d40">   29</a></span>&#160;    };</div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160; </div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;    <a class="code" href="class_tree_builder_manager.html#a1c1e9bc07025dd5160ac37277c10647a">TreeBuilderManager</a>(std::string <a class="code" href="class_tree_builder_manager.html#a4c1a65ed414d8317911abe3d4f704bf6">method</a>, std::string <a class="code" href="class_tree_builder_manager.html#a7e62c0d18ca2e9782f6e1f689b4388d4">njTmpDir</a>, std::string <a class="code" href="class_tree_builder_manager.html#ac2e2786055dddad38c1bdce4087638e8">inFile</a>, FILE *outfile, <a class="code" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68">InputType</a> <a class="code" href="class_tree_builder_manager.html#aae28e02c9576d10f1d060a9b35e948d9">inType</a>,</div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;                       <a class="code" href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17">OutputType</a> <a class="code" href="class_tree_builder_manager.html#abdf50c04e7fbf7355186615c94738940">outType</a>, <a class="code" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008">AlphabetType</a> <a class="code" href="class_tree_builder_manager.html#a3047ef12674cd2feab230d5445ec057e">alphType</a>, <a class="code" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8d">CorrectionType</a> <a class="code" href="class_tree_builder_manager.html#adf86247bbac061e015008cf779aa1922">corrType</a>, <span class="keywordtype">int</span> <a class="code" href="class_tree_builder_manager.html#ac022773150741a88a56920d768b366d4">threads</a>, <span class="keywordtype">bool</span> useSSE);</div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160; </div>
<div class="line"><a name="l00034"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#a4c1a65ed414d8317911abe3d4f704bf6">   34</a></span>&#160;    std::string <a class="code" href="class_tree_builder_manager.html#a4c1a65ed414d8317911abe3d4f704bf6">method</a>;</div>
<div class="line"><a name="l00035"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#a7e62c0d18ca2e9782f6e1f689b4388d4">   35</a></span>&#160;    std::string <a class="code" href="class_tree_builder_manager.html#a7e62c0d18ca2e9782f6e1f689b4388d4">njTmpDir</a>;</div>
<div class="line"><a name="l00036"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#ac2e2786055dddad38c1bdce4087638e8">   36</a></span>&#160;    std::string <a class="code" href="class_tree_builder_manager.html#ac2e2786055dddad38c1bdce4087638e8">inFile</a>;</div>
<div class="line"><a name="l00037"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#a0efd9a961ff0dd21dc150202ad0dab65">   37</a></span>&#160;    FILE *<a class="code" href="class_tree_builder_manager.html#a0efd9a961ff0dd21dc150202ad0dab65">outFile</a>;</div>
<div class="line"><a name="l00038"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#a5710efedbd3702d1dc95d0722e757351">   38</a></span>&#160;    std::string **<a class="code" href="class_tree_builder_manager.html#a5710efedbd3702d1dc95d0722e757351">names</a>;</div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;    <span class="comment">//Float** inD;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;    <span class="comment">//int inDsize;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#aae28e02c9576d10f1d060a9b35e948d9">   41</a></span>&#160;    <a class="code" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68">InputType</a> <a class="code" href="class_tree_builder_manager.html#aae28e02c9576d10f1d060a9b35e948d9">inType</a>;</div>
<div class="line"><a name="l00042"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#abdf50c04e7fbf7355186615c94738940">   42</a></span>&#160;    <a class="code" href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17">OutputType</a> <a class="code" href="class_tree_builder_manager.html#abdf50c04e7fbf7355186615c94738940">outType</a>;</div>
<div class="line"><a name="l00043"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#a3047ef12674cd2feab230d5445ec057e">   43</a></span>&#160;    <a class="code" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008">AlphabetType</a> <a class="code" href="class_tree_builder_manager.html#a3047ef12674cd2feab230d5445ec057e">alphType</a>;</div>
<div class="line"><a name="l00044"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#adf86247bbac061e015008cf779aa1922">   44</a></span>&#160;    <a class="code" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8d">CorrectionType</a> <a class="code" href="class_tree_builder_manager.html#adf86247bbac061e015008cf779aa1922">corrType</a>;</div>
<div class="line"><a name="l00045"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#a9ae531e04f5efb9fe8228ede332404dd">   45</a></span>&#160;    <span class="keyword">const</span> <span class="keyword">static</span> <span class="keywordtype">int</span> <a class="code" href="class_tree_builder_manager.html#a9ae531e04f5efb9fe8228ede332404dd">NUM_RAND_DIR_CHARS</a> = 6;</div>
<div class="line"><a name="l00046"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#a150db90e2abf2fc03731688eb898bbb3">   46</a></span>&#160;    std::string <a class="code" href="class_tree_builder_manager.html#a150db90e2abf2fc03731688eb898bbb3">chars</a>;</div>
<div class="line"><a name="l00047"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#ac022773150741a88a56920d768b366d4">   47</a></span>&#160;    <span class="keywordtype">int</span> <a class="code" href="class_tree_builder_manager.html#ac022773150741a88a56920d768b366d4">threads</a>;</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160; </div>
<div class="line"><a name="l00049"></a><span class="lineno"><a class="line" href="class_tree_builder_manager.html#a4c60ce04a47c306072401de1d9d83571">   49</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="class_tree_builder_manager.html#a4c60ce04a47c306072401de1d9d83571">newDistanceMethod</a>;</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160; </div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;    std::string <a class="code" href="class_tree_builder_manager.html#a82bd45375c241cc86bf5d26f4fef05ed">doJob</a>();</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;};</div>
</div><!-- fragment --></div><!-- contents -->
</div><!-- doc-content -->
<div class="ttc" id="aclass_tree_builder_manager_html_a4c60ce04a47c306072401de1d9d83571"><div class="ttname"><a href="class_tree_builder_manager.html#a4c60ce04a47c306072401de1d9d83571">TreeBuilderManager::newDistanceMethod</a></div><div class="ttdeci">bool newDistanceMethod</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:49</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_ae26c0058859fbe67055a43f55b7c5008a9cf0eb2046097228c5269e9da5e47cba"><div class="ttname"><a href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008a9cf0eb2046097228c5269e9da5e47cba">TreeBuilderManager::dna</a></div><div class="ttdeci">@ dna</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:23</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_ac2e2786055dddad38c1bdce4087638e8"><div class="ttname"><a href="class_tree_builder_manager.html#ac2e2786055dddad38c1bdce4087638e8">TreeBuilderManager::inFile</a></div><div class="ttdeci">std::string inFile</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:36</div></div>
<div class="ttc" id="a_exception_handler_8hpp_html"><div class="ttname"><a href="_exception_handler_8hpp.html">ExceptionHandler.hpp</a></div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a0efd9a961ff0dd21dc150202ad0dab65"><div class="ttname"><a href="class_tree_builder_manager.html#a0efd9a961ff0dd21dc150202ad0dab65">TreeBuilderManager::outFile</a></div><div class="ttdeci">FILE * outFile</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:37</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_ac022773150741a88a56920d768b366d4"><div class="ttname"><a href="class_tree_builder_manager.html#ac022773150741a88a56920d768b366d4">TreeBuilderManager::threads</a></div><div class="ttdeci">int threads</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:47</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_af1e010b6d69ec4c8a7860041ba823b68"><div class="ttname"><a href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68">TreeBuilderManager::InputType</a></div><div class="ttdeci">InputType</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:19</div></div>
<div class="ttc" id="a_sequence_file_reader_8hpp_html"><div class="ttname"><a href="_sequence_file_reader_8hpp.html">SequenceFileReader.hpp</a></div></div>
<div class="ttc" id="a_tree_node_8hpp_html"><div class="ttname"><a href="_tree_node_8hpp.html">TreeNode.hpp</a></div></div>
<div class="ttc" id="aclass_tree_builder_manager_html"><div class="ttname"><a href="class_tree_builder_manager.html">TreeBuilderManager</a></div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:11</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_af1e010b6d69ec4c8a7860041ba823b68a6d9503e62c1cc7af8faafe95ca03fa9f"><div class="ttname"><a href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68a6d9503e62c1cc7af8faafe95ca03fa9f">TreeBuilderManager::distance</a></div><div class="ttdeci">@ distance</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:20</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a82bd45375c241cc86bf5d26f4fef05ed"><div class="ttname"><a href="class_tree_builder_manager.html#a82bd45375c241cc86bf5d26f4fef05ed">TreeBuilderManager::doJob</a></div><div class="ttdeci">std::string doJob()</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.cpp:32</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_ae26c0058859fbe67055a43f55b7c5008a089be0a828fca4605323da2e3a171202"><div class="ttname"><a href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008a089be0a828fca4605323da2e3a171202">TreeBuilderManager::amino</a></div><div class="ttdeci">@ amino</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:23</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_ae26c0058859fbe67055a43f55b7c5008"><div class="ttname"><a href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008">TreeBuilderManager::AlphabetType</a></div><div class="ttdeci">AlphabetType</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:22</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a3047ef12674cd2feab230d5445ec057e"><div class="ttname"><a href="class_tree_builder_manager.html#a3047ef12674cd2feab230d5445ec057e">TreeBuilderManager::alphType</a></div><div class="ttdeci">AlphabetType alphType</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:43</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a4cd821248549c591777002b96d1b1f17a432f48fbf28ef0573a1a3848b5cf1d40"><div class="ttname"><a href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17a432f48fbf28ef0573a1a3848b5cf1d40">TreeBuilderManager::tree</a></div><div class="ttdeci">@ tree</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:28</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a373cf550fdc215fc25daf72e40b56a8daa48e32132856572cccb189cd72e521c7"><div class="ttname"><a href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8daa48e32132856572cccb189cd72e521c7">TreeBuilderManager::none</a></div><div class="ttdeci">@ none</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:26</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_aae28e02c9576d10f1d060a9b35e948d9"><div class="ttname"><a href="class_tree_builder_manager.html#aae28e02c9576d10f1d060a9b35e948d9">TreeBuilderManager::inType</a></div><div class="ttdeci">InputType inType</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:41</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a373cf550fdc215fc25daf72e40b56a8da78e91f6ce40102b0d61e8b9d51750638"><div class="ttname"><a href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8da78e91f6ce40102b0d61e8b9d51750638">TreeBuilderManager::JukesCantor</a></div><div class="ttdeci">@ JukesCantor</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:26</div></div>
<div class="ttc" id="a_distance_reader_8hpp_html"><div class="ttname"><a href="_distance_reader_8hpp.html">DistanceReader.hpp</a></div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a1c1e9bc07025dd5160ac37277c10647a"><div class="ttname"><a href="class_tree_builder_manager.html#a1c1e9bc07025dd5160ac37277c10647a">TreeBuilderManager::TreeBuilderManager</a></div><div class="ttdeci">TreeBuilderManager(std::string method, std::string njTmpDir, std::string inFile, FILE *outfile, InputType inType, OutputType outType, AlphabetType alphType, CorrectionType corrType, int threads, bool useSSE)</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.cpp:6</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a7e62c0d18ca2e9782f6e1f689b4388d4"><div class="ttname"><a href="class_tree_builder_manager.html#a7e62c0d18ca2e9782f6e1f689b4388d4">TreeBuilderManager::njTmpDir</a></div><div class="ttdeci">std::string njTmpDir</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:35</div></div>
<div class="ttc" id="a_tree_builder_ext_mem_8hpp_html"><div class="ttname"><a href="_tree_builder_ext_mem_8hpp.html">TreeBuilderExtMem.hpp</a></div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a5710efedbd3702d1dc95d0722e757351"><div class="ttname"><a href="class_tree_builder_manager.html#a5710efedbd3702d1dc95d0722e757351">TreeBuilderManager::names</a></div><div class="ttdeci">std::string ** names</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:38</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a9ae531e04f5efb9fe8228ede332404dd"><div class="ttname"><a href="class_tree_builder_manager.html#a9ae531e04f5efb9fe8228ede332404dd">TreeBuilderManager::NUM_RAND_DIR_CHARS</a></div><div class="ttdeci">static const int NUM_RAND_DIR_CHARS</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:45</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a4c1a65ed414d8317911abe3d4f704bf6"><div class="ttname"><a href="class_tree_builder_manager.html#a4c1a65ed414d8317911abe3d4f704bf6">TreeBuilderManager::method</a></div><div class="ttdeci">std::string method</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:34</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_abdf50c04e7fbf7355186615c94738940"><div class="ttname"><a href="class_tree_builder_manager.html#abdf50c04e7fbf7355186615c94738940">TreeBuilderManager::outType</a></div><div class="ttdeci">OutputType outType</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:42</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_adf86247bbac061e015008cf779aa1922"><div class="ttname"><a href="class_tree_builder_manager.html#adf86247bbac061e015008cf779aa1922">TreeBuilderManager::corrType</a></div><div class="ttdeci">CorrectionType corrType</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:44</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a373cf550fdc215fc25daf72e40b56a8da7bff75f1893babce718611848369ad04"><div class="ttname"><a href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8da7bff75f1893babce718611848369ad04">TreeBuilderManager::FastTree</a></div><div class="ttdeci">@ FastTree</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:26</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a373cf550fdc215fc25daf72e40b56a8da6a180df7a39a3dd2e0f2283fbdc9c9eb"><div class="ttname"><a href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8da6a180df7a39a3dd2e0f2283fbdc9c9eb">TreeBuilderManager::not_assigned</a></div><div class="ttdeci">@ not_assigned</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:26</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_af1e010b6d69ec4c8a7860041ba823b68a5496170f117c3d558853e10ccee02666"><div class="ttname"><a href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68a5496170f117c3d558853e10ccee02666">TreeBuilderManager::alignment</a></div><div class="ttdeci">@ alignment</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:20</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a373cf550fdc215fc25daf72e40b56a8dae1e7c68b84de2d982d8fc029b480cc17"><div class="ttname"><a href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8dae1e7c68b84de2d982d8fc029b480cc17">TreeBuilderManager::Kimura2</a></div><div class="ttdeci">@ Kimura2</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:26</div></div>
<div class="ttc" id="a_tree_builder_bin_heap_8hpp_html"><div class="ttname"><a href="_tree_builder_bin_heap_8hpp.html">TreeBuilderBinHeap.hpp</a></div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a150db90e2abf2fc03731688eb898bbb3"><div class="ttname"><a href="class_tree_builder_manager.html#a150db90e2abf2fc03731688eb898bbb3">TreeBuilderManager::chars</a></div><div class="ttdeci">std::string chars</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:46</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a373cf550fdc215fc25daf72e40b56a8d"><div class="ttname"><a href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8d">TreeBuilderManager::CorrectionType</a></div><div class="ttdeci">CorrectionType</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:25</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a4cd821248549c591777002b96d1b1f17a19cba20113304d5be5b0b1b3cdb11b91"><div class="ttname"><a href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17a19cba20113304d5be5b0b1b3cdb11b91">TreeBuilderManager::dist</a></div><div class="ttdeci">@ dist</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:28</div></div>
<div class="ttc" id="aclass_tree_builder_manager_html_a4cd821248549c591777002b96d1b1f17"><div class="ttname"><a href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17">TreeBuilderManager::OutputType</a></div><div class="ttdeci">OutputType</div><div class="ttdef"><b>Definition:</b> TreeBuilderManager.hpp:27</div></div>
<div class="ttc" id="a_distance_reader_ext_mem_8hpp_html"><div class="ttname"><a href="_distance_reader_ext_mem_8hpp.html">DistanceReaderExtMem.hpp</a></div></div>
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